Two homeowners in Melbourne's south-east claim construction of the State Government's sky rail project has caused serious structural damage to their homes — a claim disputed by the authority in charge.

Key points:

Nine-metre-high sections of sky rail have been built to remove Melbourne level crossings

Two homeowners claim their properties were damaged by sky rail construction works

The authority responsible said its investigation found a different cause for the damage

Ms Shakallis claims her unit has sustained "severe" structural damage since construction on that project, and an engineering report she commissioned found it was "highly possible" some of that damage was as a result of work on the sky rail in January last year.

But a separate report commissioned by the Level Crossing Removal Authority (LXRA) found the type of damage was "most likely" caused by a loss of moisture in the soil around the building after plumbing works completed two years earlier.

Ms Shakallis said repairing the damage at her unit could cost up to $20,000.

"We've got brickwork detaching from our home framing, we've got cracks in the roof that we have to tape up to stop dirt coming in and falling on us in the middle of the night," she told ABC Radio Melbourne.

"I've been engaging with [the] Level Crossing [Removal Authority] since January this year, but had no satisfactory response from them ... we would like this to be repaired, basically."

Ms Shakallis said she took up an offer from the LXRA to get a free condition report for her property, which found there was no significant damage to the house before the construction started.

"We're happy with where we live, we appreciate the work they've done because it has cleared the congestion greatly," she said.

"But we're not in a position to fix the amount of damage that's now happened to our property because of it."

After seeing the damage she commissioned an engineering report by John Kyrgios and Associates, which concluded: "We believe that it is highly possible that this cracking has occurred as a result of drilling and heavy transport travelling on the roadway".

It recommended getting another report from a geotechnical engineer, something Ms Shakallis said she could not afford.

'Problems with the soil'

In response to her complaint, the LXRA commissioned its own engineer's report by consultants Technical Assessing, which found the cracking in the property was most likely from a loss of moisture in the soil caused by various factors including a "pipe renewal" undertaken by the body corporate in early 2016.

"This independent report found that the issues at Ms Shakallis's property were not caused by project works but by underlying problems with the soil," project director Brett Summers said.

"The Caulfield to Dandenong level crossing removal project works closely with local residents and remains committed to managing or rectifying any impacts stemming from our construction activities."